Variant classification summary

NM_006218.4:c.2042G>C

PIK3CA · NP_006209.2:p.(Ser681Thr) · NM_006218.4

GRCh37: chr3:178938800 G>C · GRCh38: chr3:179221012 G>C

Gene: PIK3CA Transcript: NM_006218.4

Final call

VUS

PM2 supporting PP2 supporting

Variant details

Gene

PIK3CA

Transcript

NM_006218.4

Protein

NP_006209.2:p.(Ser681Thr)

gnomAD AF

ClinVar

Uncertain significance

OncoKB

Unknown Oncogenic Effect

Classification rationale

Interpretation summary

Generated evidence synthesis

1

PM2_Supporting: This variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada, meeting the VCEP threshold of ≤1 individual in population databases.

2

PP2_Supporting: PIK3CA has a missense constraint Z-score of 4.07 in gnomAD v2.1, exceeding the VCEP threshold of >3.09, indicating a low rate of benign missense variation.

3

PS1 is not met: no alternative nucleotide change at codon 681 producing p.Ser681Thr has been established as pathogenic.

4

PM1 is not met: residue Ser681 at position 681 falls outside the VCEP Table 4 approved kinase domains for PIK3CA (AA 322-483 and AA 797-1068).

5

PS3 and BS3 are not met: no variant-specific functional studies are available. OncoKB classifies p.Ser681Thr as Unknown Oncogenic Effect.

6

PS4 is not met: no affected individuals with this variant have been reported; no phenotype points can be scored under VCEP Tables 2A/2B.

7

Six publications were reviewed; none mention NM_006218.4:c.2042G>C or PIK3CA p.Ser681Thr.

8

Using the Brain Malformations VCEP Tavtigian point framework (Path Supporting +1, Path Moderate +2, Path Strong +4, Path Very Strong +8; Benign Supporting -1, Mod -2, Strong -4, Very Strong -8), the total score is +2 (PM2_Supporting +1, PP2_Supporting +1), which falls within the VUS range (0-5 points).

Final determination: Brain Malformations Specification Tavtigian point framework v1.1.0 point-based framework yields a total score of 2, which maps to VUS under the specified Tavtigian-style ranges.

Criteria assessment

ACMG/AMP criteria review

Criteria shown when status is available

All criteria require review: For research and educational purposes only.

Criterion	Status	Rationale	Evidence used
PVS1	N/A	Not applicable per ClinGen Brain Malformations VCEP v1.1.0: loss of function is not the disease mechanism; PIK3CA-related brain malformations are caused by gain-of-function variants.	cspec
PS1	Not met	No other nucleotide change at codon 681 producing the same amino acid substitution (p.Ser681Thr) has been established as pathogenic. This variant represents a novel missense change at this residue.	clinvar
PS2	Not met	No de novo observation reported for this variant in any available source. No evidence of absent parental genotype or tissue-specific mosaicism as required by the VCEP PS2 criteria.	clinvar
PS3	Not met	No well-established in vitro or in vivo functional studies have been performed for this specific variant. OncoKB classifies this variant as Unknown Oncogenic Effect. No functional assay meeting SVI/BMVCEP quality criteria (PMID:31892348) was identified.	oncokb
PS4	Not met	No affected individuals with this variant have been reported in the literature or clinical databases. No phenotype points can be assigned under VCEP Tables 2A/2B. While PM2 is met (absent from controls), no cases exist to score.	clinvar
PS5	Not met	PS5 is not included in the Brain Malformations VCEP specification. Under generic ACMG/AMP 2015 rules, PS5 requires a reputable source to have recently reported the variant as pathogenic. ClinVar classifies this variant as Uncertain Significance (2 clinical laboratories), which does not satisfy the criterion.	clinvar generic_acmg_combination_rules
PM1	Not met	Residue Ser681 (amino acid position 681) does not fall within the Table 4 critical functional domains for PIK3CA. The VCEP-approved domains are the kinase domains at AA 322-483 and AA 797-1068. Ser681 lies between these two domains and is not within a mutational hotspot.	cspec
PM2	Met	This variant is absent from gnomAD v2.1 (exomes), gnomAD v4.1 (exomes), and gnomAD-Canada v1.0 (genomes). Per VCEP specification, PM2 is awarded at Supporting strength when the variant is absent or present in ≤1 individual in population databases.	gnomad_v2 gnomad_v4 gnomad_canada
PM5	Not met	No pathogenic or likely pathogenic missense variant at the same amino acid residue (Ser681) was identified as a comparator. The PM5 candidate search returned zero same-residue candidates, including zero expert-panel-reviewed pathogenic variants at position 681.	pm5_candidates clinvar
PM6	N/A	Not applicable per ClinGen Brain Malformations VCEP: this point is addressed according to PS2 and will not be used. Additionally, no assumed de novo events were identified.	cspec
PP1	N/A	Not applicable per ClinGen Brain Malformations VCEP v1.1.0: disease-causing variants are germline mosaic, de novo, or mosaic, making co-segregation analysis inapplicable.	cspec
PP2	Met	PIK3CA has a missense constraint Z-score of 4.07 in gnomAD v2.1, exceeding the VCEP threshold of >3.09. This indicates a low rate of benign missense variation in PIK3CA, where missense variants are a common disease mechanism.	gnomad_v2 cspec
PP3	N/A	Not applicable per ClinGen Brain Malformations VCEP v1.1.0: traditional pathogenicity prediction algorithms focus on loss-of-function mechanisms, whereas PIK3CA-related brain malformations are caused by gain-of-function variants. Use may be revisited when algorithms specifically designed for GOF prediction become available.	cspec
PP4	N/A	Not applicable per ClinGen Brain Malformations VCEP v1.1.0: this criterion is accounted for under PS4 in the VCEP framework.	cspec
PP5	N/A	Not applicable per ClinGen Brain Malformations VCEP v1.1.0: this criterion is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee.	cspec
BA1	Not met	Variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada. The VCEP BA1 threshold is >0.0926% allele frequency. This variant's population frequency is 0%, far below the threshold.	gnomad_v2 gnomad_v4 gnomad_canada
BS1	Not met	Variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada. The VCEP BS1 threshold is >0.0185% allele frequency. This variant's population frequency is 0%, far below the threshold.	gnomad_v2 gnomad_v4 gnomad_canada
BS2	Not met	No homozygotes are present in gnomAD and no well-phenotyped heterozygous family members have been reported. The VCEP requires ≥3 homozygotes in gnomAD or ≥3 well-phenotyped heterozygous family members.	gnomad_v2 gnomad_v4 gnomad_canada
BS3	Not met	No well-established in vitro or in vivo functional studies demonstrate no damaging effect for this specific variant. Functional evidence for p.Ser681Thr is absent from the literature and curated databases.	oncokb
BS4	N/A	Not applicable per ClinGen Brain Malformations VCEP v1.1.0: not applicable as these are de novo, germline mosaic, or post-zygotic mutations.	cspec
BP1	N/A	Not applicable per ClinGen Brain Malformations VCEP v1.1.0: loss of function is not the disease mechanism for PIK3CA-related brain malformations.	cspec
BP2	Not met	No evidence that this variant has been observed in cis or trans with a known pathogenic variant in PIK3CA. No phase information is available.
BP4	N/A	Not applicable per ClinGen Brain Malformations VCEP v1.1.0: BP4 is restricted to synonymous, intronic (except canonical splice sites), and non-coding UTR variants. This is a missense variant (c.2042G>C, p.Ser681Thr).	cspec
BP5	Not met	No evidence that this variant has been found in a case with an alternate molecular basis for disease. No co-occurring explanatory variant has been reported.
BP6	N/A	Not applicable per ClinGen Brain Malformations VCEP v1.1.0: this criterion is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee.	cspec
BP7	N/A	Not applicable per ClinGen Brain Malformations VCEP v1.1.0: BP7 is restricted to synonymous, intronic (except canonical splice sites), and non-coding UTR variants. This is a missense variant (c.2042G>C, p.Ser681Thr).	cspec

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